get counts by gene for single cell rna seq
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9 weeks ago
das2000sidd ▴ 30

Hi

I have just got started with single cell RNA seq and I have two queries. One is how do I combine my dataset and an externally downloaded dataset for subsequent dimension reduction usage such as UMAP? I have the matrix, barcode and features file for both the datasets.

How do I get count by gene from a single cell RNA from the object read using Seurat. If count_data was an object read in by Read10X of Seurat object, then I see i can access the genes using count_data@Dimnames[[1]] and the count matrix using count_data@meta.data. But I am not sure how to get the counts by gene.

Any help would be much appreciated.

Thanks!

rna-seq single cell rna seq Tool • 122 views
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Hi, can you confirm that you read https://satijalab.org/seurat/articles/essential_commands.html and then say where you get stuck?

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